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By Trapnell C., Pachter L. , Last update 1494698999
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cuffdiff description

Cuffdiff finds significant changes in transcript expression, splicing, and promoter use

Parent program: cufflinks

Cufflinks is a software for estimation of gene expression levels. It performs reference-guided assembly of aligned RNA-seq reads into a set of transcripts and then evaluates the relative abundances of these transcripts by counting supporting reads. Cufflinks is a part of the Tuxedo protocol for RNA-Seq data processing. It is recommended to use Tophat output RNA-seq read alignment file in SAM or BAM format as input, but Cufflinks can accept SAM or BAM files created by any read mapper.